Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate PP_2589 PP_2589 Aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Putida:PP_2589 Length = 497 Score = 378 bits (971), Expect = e-109 Identities = 205/468 (43%), Positives = 293/468 (62%), Gaps = 4/468 (0%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTANER 73 IDGK V + DG TF INPAT L VA G AE+DLAV +A++A GPW +M ER Sbjct: 22 IDGKPVNAQDGATFAAINPATNNVLAQVAACGHAEVDLAVASARRAFEQGPWPRMAPGER 81 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 VL ++ +LI+ +EEL++L+SL+ GKP + +ID+P +A+ F ++ + + + ++ Sbjct: 82 KKVLLRLAELIMAHREELALLDSLNMGKPVMDAYNIDVPGSAHVFAWYGEALDKLYDQVA 141 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 AL R +GV+ + PWN PL + WKLAPALAAGN+VV+KPAE +P +A L Sbjct: 142 PTAANALATITREALGVVAAVVPWNFPLDMAAWKLAPALAAGNSVVLKPAEQSPFSALRL 201 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMA-SAAKTLK 252 A++ +AGVP+GV+N+V G G AG AL HPDV+ + FTG T GK M SA LK Sbjct: 202 AQLALEAGVPEGVLNVVPGLG-EQAGQALGLHPDVDCLVFTGSTQVGKYFMQYSAQSNLK 260 Query: 253 RLSYELGGKNPNVIFAD-SNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 ++ E GGK+PN++F + +LD E F NQGEVC SR+YV+R ++ F+E+ Sbjct: 261 QVWLECGGKSPNLVFDNCQDLDLAAEKAAFGIFFNQGEVCSANSRLYVQRAIHDEFIERL 320 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYF 371 AK ++ + G+P D ++ GA++ R+ I A +EG ++ GG+R + Sbjct: 321 QAKARQWLPGNPLDPASRAGAIVDAGQTGRIEAAIVRAGQEGARLVCGGRRLTIEGSDNY 380 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 +EPTI G+ + +EE+FGPV+ V FDTEEE + ND+ YGL+ASVW++D + H Sbjct: 381 IEPTIFAGVEGRMSLAREEVFGPVLAVSAFDTEEEAVRLANDSIYGLAASVWSDDFNQVH 440 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSEL 479 RVA ++AG V VNT D+ PFGG KQSG GR+ LHSF+ YS+L Sbjct: 441 RVARALKAGTVSVNTVDALDVTVPFGGGKQSGFGRDLSLHSFDKYSQL 488 Lambda K H 0.318 0.136 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 591 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 486 Length of database: 497 Length adjustment: 34 Effective length of query: 452 Effective length of database: 463 Effective search space: 209276 Effective search space used: 209276 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory